Huntington's disease is a devastating neurodegenerative disease caused by CAG codon expansion in exon 1 of the huntingtin (htt) gene. Similar CAG repeat expansions in eight other proteins are associated with eight different neurodegenerative diseases. In all nine diseases, the CAG repeat expansions encode polyglutamine expansions in the protein products, and the onset and severity of disease are inversely correlated with the polyglutamine length although the quantitative nature of this correlation is different for each of the nine disorders. Polyglutamine expansions end up in insoluble neuronal inclusions and there is growing evidence that the mechanisms of aggregation and the soluble oligomeric species are directly linked to selective neurodegeneration in each of the nine diseases. Polyglutamine expansions destabilize their host proteins and increase the likelihood of proteolysis. Fragments of proteolysis consist of polyglutamine tracts and flanking N- and C-terminal segments. The N- and C-terminal segments that flank the polyglutamine stretch are unique to each disease-related protein. Driving forces for aggregation of homopolymeric polyglutamine becomes stronger with increasing chain length and naturally occurring N- and C-terminal flanking sequences modulate this driving force. Our goal is to understand how sequences that flank polyglutamine expansions in disease-related proteins modulate the intrinsic, length-dependent conformational preferences and aggregation mechanisms of polyglutamine. Our approaches are based on a combination of novel atomistic simulations and a panel of in vitro experiments. Our recent results are consistent with the hypothesis that naturally occurring flanking sequences can act as gatekeepers to suppress intrinsic aggregation propensities of aggregation-prone regions. Therefore, the current proposal is guided by the following hypothesis: Naturally occurring flanking sequences in disease-related proteins can act as gatekeepers to decrease the intrinsic aggregation tendencies of polyglutamine tracts. This effect can be overcome by expansion mutations that lead to increased polyglutamine lengths. Additionally, gatekeeping mechanisms likely vary with flanking sequence, giving rise to differences in gatekeeping efficiencies. We will use a combination of novel atomistic simulations and in vitro experiments to characterize 1) conformational changes within different naturally occurring terminal flanking sequences and the coupling between these changes and the degree of sequestration / exposure of aggregation-prone polyglutamine regions within intramolecular interfaces as a function of polyglutamine length and 2) if naturally occurring flanking sequences are bona fide gatekeepers and to quantify the degree to which these sequences modulate aggregation as a function of polyglutamine length. Precise understanding of the mechanisms of coupling between flanking sequences and polyglutamine expansions will allow us to identify targets for inhibition of routes to aggregation-mediated toxicity and neurodegeneration.